nf-core/clipseq
CLIP sequencing analysis pipeline for QC, pre-mapping, genome mapping, UMI deduplication, and multiple peak-calling options.
22.10.6.
Learn more.
Define where the pipeline should find input data and save output data.
Input FastQ files.
stringThe output directory where the results will be saved.
string./resultsEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Options for the reference genome indices used to align reads.
Name of iGenomes reference.
stringOrganism for small RNA reference.
stringPath to small RNA FASTA file
stringPath to genome FASTA file.
stringPath to genome FASTA index file
stringPath to GTF annotation file
stringPath to genome STAR index
stringSave STAR index if generated within pipeline.
booleanDirectory / URL base for iGenomes references.
strings3://ngi-igenomes/igenomes/Do not load the iGenomes reference config.
booleanDefine sequencing adapters and UMI options
Sequencing adapter for trimming
stringAGATCGGAAGAGCUMI format to move to FastQ header (optional)
stringFalseDeduplicate using UMIs
booleantrueUMI separator in the FastQ read name
string:Define peak callers and peak calling options
Which peakcaller(s) to use
stringPath to iCount segment file
stringiCount half-window setting
integer3iCount merge-window setting
integer3Paraclu minimum cluster count
integer10Paraclu minimum density increase
integer2Paraclu maximum cluster length
integer200PureCLIP binding characteristics of protein
integerPureCLIP merge distance
integer8PureCLIP chromosomes for HMM training
stringallPiranha bin size
integer3Piranha clustering distance
integer3Define motif finding parameters
Perform motif finding
booleanSample n peaks for motif finding
integer1000Less common options for the pipeline, typically set in a config file.
Display help text.
booleanMethod used to save pipeline results to output directory.
stringBoolean whether to validate parameters against the schema at runtime
booleantrueEmail address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Send plain-text email instead of HTML.
booleanFile size limit when attaching MultiQC reports to summary emails.
string25.MBDo not use coloured log outputs.
booleanCustom config file to supply to MultiQC.
stringDirectory to keep pipeline Nextflow logs and reports.
string${params.outdir}/pipeline_infoShow all params when using --help
booleanSet the top limit for requested resources for any single job.
Maximum number of CPUs that can be requested for any single job.
integer16Maximum amount of memory that can be requested for any single job.
string128.GB^[\d\.]+\s*.(K|M|G|T)?B$Maximum amount of time that can be requested for any single job.
string240.h^[\d\.]+\.*(s|m|h|d)$Parameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
stringmasterBase directory for Institutional configs.
stringhttps://raw.githubusercontent.com/nf-core/configs/masterInstitutional configs hostname.
stringInstitutional config name.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
string